Does tuning affect intonation?
No. Intonation is defined by the physical positions of the nut, frets and saddle. Since chaging tunings involves only the tension of the strings, you'll be just fine.
What causes guitar intonation problems?
As you use your guitar strings, the fret wire wears down the strings. Eventually, you might notice some flat spots on the underside of the strings that line up to the frets. This can gradually cause intonation problems as the way the string makes contact with the fret changes.